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Gene networks were constructed based on the Ingenuity knowledge base.
The reference set was genes from the Ingenuity Knowledge Base including all species, tissues, and cell lines.
Lower-level functions, classified within these categories, are assigned p-values and come from findings within the Ingenuity Knowledge Base.
The network genes associated with biological functions and/or diseases in the Ingenuity knowledge base were considered for the analysis.
Network interactions were inferred using the Ingenuity Knowledge Base of pre-curated molecular and functional interactions mined from published literature.
Human, mouse, and rat orthologs of a gene are stored as separate objects in the Ingenuity knowledge base, but are represented as a single node in the network.
All edges are supported by at least 1 reference from the literature, from a textbook, or from canonical information stored in the Ingenuity knowledge base.
For analysis with Ingenuity, these genes, were designated as focus genes and were overlaid onto a global molecular network developed from information contained in the Ingenuity knowledge base.
IPA generates networks based on the connectivity of genes in the data set using Ingenuity Knowledge Base, which is mostly dependent on scientific literature.
Genes from the dataset with a 1.41 fold change (log2 ratio ±0.5) were associated with a canonical pathway in the Ingenuity knowledge base and considered for the analysis.
A core analysis was run employing direct relationships only, the Ingenuity knowledge base genes as the reference set, and with down-regulators as the defined expression value parameter.
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CEO of Professional Science Editing for Scientists @ prosciediting.com